Merge changes from develop

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,30 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behaviour, including the
+1. Command executed
+2. Error message
+
+**Expected behaviour**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. Ubuntu]
+ - OS version [e.g. 20.04 LTS]
+ - Python version [e.g. 3.7]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/custom.md

@@ -0,0 +1,10 @@
+---
+name: Custom issue template
+about: Describe this issue template's purpose here.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/codeql.yml

@@ -0,0 +1,76 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "develop" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "develop" ]
+  schedule:
+    - cron: '34 3 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Use only 'java' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/pypi-publish.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/testing_python_app.yml

@@ -2,9 +2,9 @@ name: CI
 
 on:
   push:
-    branches: [ master ]
+    branches: [ develop ]
   pull_request:
-    branches: [ master ]
+    branches: [ develop ]
 
 
 jobs:
@@ -14,16 +14,16 @@ jobs:
 
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: [macos-12, ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: "actions/checkout@v2"
+      - uses: "actions/checkout@v3"
         with:
           fetch-depth: 0
 
       # Setup env
-      - uses: "actions/setup-python@v2"
+      - uses: "actions/setup-python@v3"
         with:
             python-version: "${{ matrix.python-version }}"
 
@@ -35,10 +35,11 @@ jobs:
       - name: "Generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
         run: |
           pip install pytest pytest-cov
-          pytest --cov=tests --cov-report=xml --cov-append
+          pytest --cov=graphbin --cov-report=xml --cov-append
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           file: coverage.xml
           fail_ci_if_error: true

.github/workflows/testing_python_conda.yml

@@ -0,0 +1,46 @@
+name: CI conda
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+
+
+jobs:
+  tests:
+    name: "Python ${{ matrix.python-version }}"
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    strategy:
+      matrix:
+        os: [macos-12, ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: "actions/checkout@v3"
+        with:
+          fetch-depth: 0
+
+      # Setup conda env
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: graphbin
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: "Setup graphbin on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+
+      - name: "Generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          pip install pytest pytest-cov
+          pytest --cov=graphbin --cov-report=xml --cov-append
+

CONTRIBUTING.md

@@ -0,0 +1,67 @@
+# Contributing to GraphBin project
+
+We love to have your contributions to the GraphBin project, whether it's:
+* Reporting a bug
+* Submitting a fix
+* Proposing new features
+
+## Clone and install GraphBin onto your machine
+
+First, make sure you have [git](https://github.com/git-guides/install-git) installed on your machine.
+
+On GitHub, [fork](https://docs.github.com/en/get-started/quickstart/fork-a-repo) the GraphBin repository and [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) it to your machine.
+
+```
+# clone repository to your local machine
+git clone https://github.com/metagentools/GraphBin.git
+```
+
+Move to the GraphBin directory and install GraphBin via [flit](https://pypi.org/project/flit/).
+
+```
+# go to repo direcotry
+cd GraphBin
+
+# install flit
+pip install flit
+
+# install graphbin via flit
+flit install -s --python `which python`
+```
+
+## Test GraphBin installation
+
+Use the following command to run [pytest](https://docs.pytest.org/en/7.1.x/) and the all the tests should pass.
+
+```
+pytest
+```
+
+## Coding Style
+
+We adhere to the [PEP 8](https://peps.python.org/pep-0008/) style guide. 
+
+Before committing, make sure to run [`black`](https://pypi.org/project/black/) and [`isort`](https://pypi.org/project/isort/).
+
+## Report bugs using Github's issues
+
+We use GitHub issues to track public bugs. Report a bug by opening a new issue in GitHub [issues](https://github.com/metagentools/GraphBin/issues). You will get to select between templates for bug report and feature request.
+
+## Committing code
+
+Once you have finished coding and all the tests pass, commit your code and make a pull request. Make sure to follow the commit style of [c3dev](https://github.com/cogent3/c3dev/wiki#style-for-commit-messages).
+
+```
+git commit -m "<commit message>"
+git push
+```
+
+Your contribution will be reviewed before accepting it. 
+
+## License
+
+By contributing, you agree that your contributions will be licensed under the BSD-3 License.
+
+## References
+
+This document was adapted from the open-source contribution guidelines for [Transcriptase](https://github.com/briandk/transcriptase-atom/blob/master/CONTRIBUTING.md) and [c3dev](https://github.com/cogent3/c3dev/wiki/How-to-Contribute-Code).